This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Abstract

Objective: Bringing together genomics, transcriptomics, proteomics, and other –omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate data faster than it can be interpreted. Materials and Methods: We have developed PANDA ( P athway AND A nnotation) Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB. PANDA represents data/annotations as icons in the graph while maintaining the other data elements (i.e. other columns for the table of annotations). Custom pathways from underrepresented diseases can be imported when existing data sources are inadequate. PANDA also allows sharing annotations among collaborators. Results : In our first use case, we show how easy it is to view supplemental data from a manuscript in the context of a user’s own data. Another use-case is provided describing how PANDA was leveraged to design a treatment strategy from the somatic variants found in the tumor of a patient with metastatic sarcomatoid renal cell carcinoma. Conclusion : PANDA facilitates the interpretation of gene-centric annotations by visually integrating this information with context of biological pathways. The application can be downloaded or used directly from our website http://bioinformaticstools.mayo.edu/research/panda-viewer/.

Author Comment

This is a submission to PeerJ for review.

Additional Information

Competing Interests

The authors declare they have no competing interests.

Author Contributions

Steven N Hart conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Raymond M Moore performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Michael T Zimmermann performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Gavin R Oliver performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Jan B Egan performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Alan H Bryce performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Jean-Pierre A Kocher conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Funding

This research project was funded by the Center for Individualized Medicine at Mayo Clinic. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Follow this preprint for updates

"Following" is like subscribing to any updates related to a preprint.
These updates will appear in your home dashboard each time you visit PeerJ.

You can also choose to receive updates via daily or weekly email digests.
If you are following multiple preprints then we will send you
no more than one email per day or week based on your preferences.

Note: You are now also subscribed to the subject areas of this preprint
and will receive updates in the daily or weekly email digests if turned on.
You can add specific subject areas through your profile settings.